苏姜猪mtDNA D-loop序列的遗传多样性分析

doi:10.16431/j.cnki.1671-7236.2023.04.019

Abstract

Abstract: 【Objective】 By obtaining and comparing the partial sequence of mtDNA D-loop hypervariable region Ⅰ of Sujiang pig,the germplasm resource characteristics and genetic diversity of Sujiang pig population were revealed.【Method】 Ear tissues of 100 parturient sows from the core group of Sujiang pigs were collected and DNA were extracted.And gene fragments of mtDNA D-loop hypervariable region Ⅰ of sows in the core group of Sujiang pigs were amplified and sequenced.The NCBI online BLAST was used to compare and calibrate the sequencing and reference sequences,and homologous sequences were found to determine the length and location of the sequence of high variable region Ⅰ of mtDNA D-loop.DnaSP v.5.10.1 software was used to calculate the number of nucleotide polymorphic sites and mutation sites in the population and the haplotype diversity (Hd),nucleotide polymorphism (Pi),average nucleotide difference (K) and other parameters were analyzed.The genetic distance of the sample was calculated based on Kimura’s 2-prarmetermodel using Mega 7.0 software and the genetic distance between different haplotypes of Sujiang pig mtDNA D-loop region sequences were obtained.The phylogenetic tree was constructed by using Neighbor-Joining (NJ) on the mtDNA D-loop hypervariable region Ⅰ sequences of 4 haplotypes of Sujiang pig,17 Chinese pig breeds and European domestic pigs (accession No.:AF034253.1).【Result】 The highly variable region Ⅰ of mtDNA D-loop sequence of 100 Sujiang pigs was amplified and sequenced,and the effective sequence with a length of 429 bp was obtained,in which the content of AT was 63.1%,and the content of GC was 36.9%,neutral test Tajima’s D value was -1.80517 (P＜0.05).It was confirmed that Sujiang pig population significantly deviated from neutral test.A total of 19 mutation sites were detected in the sequencing column,and 4 haplotypes were defined,Hd was 0.578,Pi was 0.0032, and the average genetic distance between the four haplotypes in the population ranged from 0.004 to 0.031.Phylogenetic tree results showed that the joining group were divided into two groups:Domestic and foreign.The four haplotypes of Sujiang pig were clustered in the domestic branch,among which haplotype H2 and Erhuface pig were clustered in the same group,and haplotype H4 was clustered in the same group with Jiangquhai and Wannanhua pig.【Conclusion】 The proportion of polymorphic sites in the high variation region Ⅰ of mtDNA D-loop in Sujiang pig population was high,Hd was high,and Pi was low.The genetic distance of dominant haplotypes in Sujiang pig population was relatively close,and the proportion of dominant haplotypes was high,which reflected that there were fewer maternal sources in Sujiang pig population.

Key words: Sujiang pig; mtDNA D-loop; genetic variation; haplotype diversity; nucleotide diversity

CLC Number:

S828

HAN Dayong, ZHOU Chunbao, NI Ligang, CHEN Zhangyan, ZHAO Jinming. Genetic Diversity of mtDNA D-loop Sequence in Sujiang Pig[J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(4): 1472-1479.

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Genetic Diversity of mtDNA D-loop Sequence in Sujiang Pig

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